[DOCS] Biological sample contribution

mehta-lab / recOrder

3D quantitative label-free imaging with phase and polarization

BSD 3-Clause "New" or "Revised" License

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[DOCS] Biological sample contribution #433

Closed talonchandler closed 12 months ago

talonchandler commented 1 year ago

Our README should lead with biological data that's available via a sample contribution. I've added this to an 0.4.1 release milestone (I'm flexible on its name).

[x] decide on a specific sample contribution, possibly zebrafish embryo or full-zebrafish data TBD
[x] truncate the dataset to a manageable download size: I think 100 MB is a good target, as long as the size is labelled clearly in the sample contribution menu
[x] upload the dataset to zenodo
[x] add the sample contribution in recOrder
[x] add a figure and/or gif of the data to recOrder's README

talonchandler commented 1 year ago

Here's a nomination for a landing-page movie.

https://github.com/mehta-lab/recOrder/assets/9554101/8b9ad343-ee5b-4648-88a9-a5c3bfa5ed6d

The phase reconstructions didn't come out looking very good for this sample (likely driven by strong absorption), so I excluded it.

@mattersoflight let's discuss this next week and we can decide on how we should proceed with this dataset, and what other datasets we might consider.

talonchandler commented 1 year ago

I'm uploading movies to this thread, so that they can be linked from the README.

https://github.com/mehta-lab/recOrder/assets/9554101/cc71da57-df6f-401b-a955-796750a96d88

https://github.com/mehta-lab/recOrder/assets/9554101/aa2180af-607f-4c0c-912c-c18dc4f29432

talonchandler commented 12 months ago

Uploading another movie for inclusion in the README

https://github.com/mehta-lab/recOrder/assets/9554101/70afb05a-1eb7-4019-9c42-af3e07bef723